FastQCFastQC Report
Thu 27 Oct 2016
H3NFYBCXY_l02n01_smallrna_ctrl1h_rep3_shoot.3510000006bfc1.fastq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameH3NFYBCXY_l02n01_smallrna_ctrl1h_rep3_shoot.3510000006bfc1.fastq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences33170926
Sequences flagged as poor quality0
Sequence length51
%GC53

[OK]Per base sequence quality

Per base quality graph

[OK]Per tile sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[WARN]Per base sequence content

Per base sequence content

[WARN]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[OK]Sequence Length Distribution

Sequence length distribution

[FAIL]Sequence Duplication Levels

Duplication level graph

[FAIL]Overrepresented sequences

SequenceCountPercentagePossible Source
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTCGTATGCC24162387.284204245609543RNA PCR Primer, Index 4 (100% over 51bp)
TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT3667971.1057785965938967RNA PCR Primer, Index 1 (100% over 30bp)
ATCCAGCCCCGCGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAAC3289770.9917630879523834RNA PCR Primer, Index 1 (100% over 24bp)
AGGGCTATAGCTCAGTTCGGTAGAGCAACTCGTTTACACCGAGATGGAATT2783910.8392620694399668No Hit
GCCCCGCGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCCAG2618740.7894684640398643RNA PCR Primer, Index 1 (100% over 29bp)
AGCCCCGCGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCCA2400530.7236849522982868RNA PCR Primer, Index 1 (100% over 28bp)
TAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTG1960060.5908969800843064RNA PCR Primer, Index 2 (97% over 35bp)
TCTCGGACCAGGCTTCATTCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT1946960.5869477385105257RNA PCR Primer, Index 1 (100% over 30bp)
TCCAGCCCCGCGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACT1890830.5700262935077544RNA PCR Primer, Index 1 (100% over 25bp)
CAGCCCCGCGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCC1646880.49648297427693155RNA PCR Primer, Index 1 (100% over 27bp)
CAGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAACTCCA1637020.4935104916878112RNA PCR Primer, Index 1 (100% over 28bp)
CCAGCCCCGCGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTC1599670.48225063117020006RNA PCR Primer, Index 1 (100% over 26bp)
CACACGACTCTCGGCAACGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA1578130.475756992735144RNA PCR Primer, Index 1 (100% over 32bp)
GTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAGGCCATGGAATTCT1452670.437934714273578No Hit
TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT1253450.3778760954698702RNA PCR Primer, Index 1 (100% over 30bp)
CGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAGGCCATGGAATTC1136560.342637404816495No Hit
GATCCAGCCCCGCGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAA1048410.3160629281196431RNA PCR Primer, Index 1 (100% over 23bp)
TATCGAGTAGACCCTGTCGTTGTGAGATGGAATTCTCGGGTGCCAAGGAAC1004500.3028254321269174RNA PCR Primer, Index 1 (100% over 24bp)
GGTAGTTCGACCGTGGAATTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC884250.2665738062301909RNA PCR Primer, Index 1 (100% over 31bp)
TCCGTTGTAGTCTAGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTG826200.24907354108836152RNA PCR Primer, Index 2 (97% over 35bp)
CACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACTC806080.2430079883811504RNA PCR Primer, Index 1 (100% over 26bp)
TCCACAGGCTTTCTTGAACTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT771210.23249577054315576RNA PCR Primer, Index 1 (100% over 30bp)
GTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATG754300.2273979327559321No Hit
TCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGG717570.2163249829082251No Hit
TTGACAGAAGAGAGTGAGCACTGGAATTCTCGGGTGCCAAGGAACTCCAGT696200.20988259417298147RNA PCR Primer, Index 1 (100% over 30bp)
CACACGACTCTCGGCAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC662930.19985272645086843RNA PCR Primer, Index 1 (100% over 33bp)
TCCGTTGTAGTCTAGCTGGTTAGGATACTTGGAATTCTCGGGTGCCAAGGA599770.18081195562644228RNA PCR Primer, Index 1 (100% over 22bp)
GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGATGGAATTCTCGGGTGC596250.17975078537150274No Hit
CGGGGTTCGTTTCCCCGGATGCGCACCATGGAATTCTCGGGTGCCAAGGAA587040.17697425751695928RNA PCR Primer, Index 1 (100% over 23bp)
CTGGGCGTCACGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGACC584040.1760698510496813RNA PCR Primer, Index 4 (100% over 38bp)
TCCGTTGTAGTCTAGCTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAGG561430.16925364097462942Illumina Small RNA Adapter 2 (100% over 21bp)
TATCGAGTAGACCCTGTCGTTGTGAGAATTTGGAATTCTCGGGTGCCAAGG547740.16512653279561745Illumina Small RNA Adapter 2 (100% over 21bp)
CCGGGGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCT547440.16503609214888967RNA PCR Primer, Index 4 (100% over 43bp)
ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGGAATTC543490.16384529030030695No Hit
CCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAGGCCATGGAATT538130.1622294174121036No Hit
TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG526970.15886502535382943No Hit
CACACGACTCTCGGCAACGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT524290.15805708890972775RNA PCR Primer, Index 1 (100% over 30bp)
GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG493320.14872059947919453Illumina Small RNA Adapter 2 (100% over 21bp)
TCCGTTGTAGTCTAGCTGGTTAGGATATGGAATTCTCGGGTGCCAAGGAAC475320.1432941606755265RNA PCR Primer, Index 1 (100% over 24bp)
GCGACCCCAGGTCAGGCGGGACTTGGAATTCTCGGGTGCCAAGGAACTCCA473320.1426912230306745RNA PCR Primer, Index 1 (100% over 28bp)
CATCGGTTCAAATCCGATAGTCGGCTCCATGGAATTCTCGGGTGCCAAGGA471790.14222997573236273RNA PCR Primer, Index 1 (100% over 22bp)
CTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA455300.137258754850558No Hit
TCCGTTGTAGTCTAGCTGGTTAGGATACTGGAATTCTCGGGTGCCAAGGAA443630.13374061369284657RNA PCR Primer, Index 1 (100% over 23bp)
GGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTAT428410.12915225821552284No Hit
CACACGACTCTCGGCAACGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC420140.1266591110540598RNA PCR Primer, Index 1 (100% over 31bp)
TATCGAGTAGACCCTGTCGTTGTGAGTGGAATTCTCGGGTGCCAAGGAACT416840.12566426394005403RNA PCR Primer, Index 1 (100% over 25bp)
GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCAA411680.12410868481633586No Hit
AGATCCAGCCCCGCGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGA411410.12402728823428083RNA PCR Primer, Index 1 (100% over 22bp)
TGCCACGATCCACTGAGATCCAGCCCCGCGTCGCACGGATTCGTTGGAATT390020.11757887012258866No Hit
CACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAAC385040.11607755538690719RNA PCR Primer, Index 1 (100% over 24bp)
TATCGAGTAGACCCTGTCGTTGTGAGAATTGGAATTCTCGGGTGCCAAGGA382030.11517013423140493RNA PCR Primer, Index 1 (100% over 22bp)
GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGGAATT364480.10987935639782861No Hit
CTGCCACGATCCACTGAGATCCAGCCCCGCGTCGCACGGATTCGTTGGAAT363060.10945127066998371No Hit
GTCGGCGCAGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGACCA356930.10760326678851233RNA PCR Primer, Index 4 (100% over 39bp)
GTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTTGGAATTCTCGGGTGCCA346240.10438056507677837No Hit
CACACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAAG332990.10038610317963388No Hit

[FAIL]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
CGTTTAC328450.044.4339731
CACACGA785700.044.3652571
AGGGCTA367400.044.3488661
GTTTACA329100.044.33254232
TACACCG321450.044.3237635
AGCTCAG617650.044.2855649
CTATAGC366800.044.2289545
TTACACC327000.044.22508234
TTCGGTA343750.044.2237616
TTTACAC330100.044.19824233
TATAGCT381400.044.175726
TATCGAG509100.044.1406171
GAGCAAC338700.044.10556823
TCGTTTA331600.044.05258630
CACCGAG321500.044.02382337
TCGAGTA509950.043.985353
TAGACCC510000.043.8708238
ACTCGTT337650.043.849628
CACAGGC111150.043.8014343
GTAGACC513050.043.759057
Produced by FastQC (version 0.11.2)